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Why do I get a different amount of Calories when I use the 4-4-9 calculation?

There are six ways to calculate Calories for a label, three of the most popular being the 4-4-9 formula, 4-4-9 adjusted for fiber, and Atwater Factors.  Manufacturers often use 4-4-9 or 4-4-9 adjusted for fiber, and the USDA uses Atwater Factors. 
 
To calculate using 4-4-9, which are average conversion factor values, the following formula is used:
  · Protein grams x 4 = Cals from Protein
  · Carbohydrate grams x 4 = Cals from Carbs
  · Fat grams x 9 = Cals from Fat
 
ESHA does not use 4-4-9 to calculate Calories.  Read more in this KB article: 4-4-9: Do you use 4-4-9 to calculate calories from the grams of carbohydrate protein and fat

Atwater Factors tend to be more precise.  Different foods have differing caloric contributions per gram.  For example, 1g of fat from one food may yield 8.4 Calories, while 1g of fat from another food may yield 9.37 Calories.  For fat, the values range very near 9 Calories, but it is not exactly 9 Calories.  Same concept with a gram of Protein or Carbohydrate.  Generally you'll find Atwater Factors to result in slightly less total Calories than when you approximate using 4-4-9.

Example of calculations for Great Northern Beans using the 4-4-9 vs Atwater formulas, based on the following:
36 grams beans containing
  · 22.2g Carbs
  · 7.8g Protein
  · 0.26g Fat
  · 13.3g Fiber
 
Using Atwater Factors:
  · 22.2g x 4.07 = 90 Cals from Carbs
  · 7.8g x 3.47 = 27 Cals from Protein
  · 0.26g x 8.37 = 2 Cals from Fat
  · Total = 119 Cals
 
Using 4-4-9 formula:
  · 22.2g x 4 = 89 Cals from Carbs
  · 7.8g x 4 = 31 Cals from Protein
  · 0.26g x 9 = 2 Cals from Fat
  · Total = 122 Cals
 
Finally, when displaying Calories on a Nutrition Facts panel, the Calories value is rounded according to NLEA rounding rules (further skewing the discrepency). 

As best practice, view your Spreadsheet report for every Recipe.  The Spreadsheet details the nutrients contributed by each ingredient.  When reporting values on the Spreadsheet, the program simply totals each column -- so total Calories is purely a sum of the calculated Calories from each ingredient.

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